Photodynamic inactivation (PDI) has been investigated to cope with the increasing incidence of multidrug-resistant (MDR) pathogens. In Hong Kong, methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are the two commonest MDR pathogens. Here, we studied the photodynamic inactivation (PDI) mediated by poly-L-lysine chlorin(e6) conjugate (pL-ce6) and toluidine blue O (TBO) in clinical MRSA and ESBL producing E. coli, together with their corresponding American Type Culture Collection (ATCC) strains. Both pL-ce6 and TBO mediated a light-and drug dose-dependent efficacy for the four pathogens. pL-ce6 was more effective. pL-ce6 at 8 µM, 30 Jcm −2 , attained 5 log killing for ESBL-producing E. coli and E. coli (ATCC 25922); 4 log killing for MRSA, and 3 log killing for S. aureus (ATCC 25923). TBO at 80 µM, 30 Jcm −2 , only exhibited 3 log killing in MRSA and 2 log killing in S. aureus (ATCC 25923). TBO (400 µM, 30 Jcm −2 ) induced equal killing for ESBLproducing E. coli and E. coli (ATCC 25922). Our studied MRSA isolate responded better than S. aureus (ATCC 25923). Thus, pL-ce6-mediated PDI in other MRSA isolates deserves further investigation.